Wonky Pickup Mounting Screws

I've had my mim jazz for about 3 years now, and finally decided to replace the pickups. got a set of EMG-J from ebay.....

now the pickup screws were not in the right place for the stock pickups....they didn't move up and down at all on the screws, and tightening the screws put lots of pressure on the pickups, instead of just moving them up and down.

now that i put in new pickups, the misalignment is even more apparent. i could barely mount the bloody pickups, let alone have any kind of useful height adjustment.

i want to drill new holes. would it be ok to drill the existing holes bigger (1/4" or 1/2"), glue dowel pieces in and redrill? or is it not good to mount pickups in the endgrain of dowel? i'm pretty sure i can get access to a drill press to ensure verticality (new word), but i'm just wondering if anyone's had to do this to their bass and if it's a good idea...